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The crystal structure of D-mandelate dehydrogenase
Analyse The crystal structure of D-mandelate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFI
- Type
- protein
- Length
- 623 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydropantoate 2-reductase
- EC
- 1.1.1.169
- UniProt
- E3USM3
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 311 | 49% helix, 19% strand | E3USM3 |
| B | 2-dehydropantoate 2-reductase (EC 1.1.1.169) | protein | 312 | 48% helix, 19% strand | E3USM3 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.51 | 0.76 | 36 | empty |
| 2 | 130 | 0.44 | 0.77 | 22 | empty |
| 3 | 94 | 0.43 | 0.79 | 20 | empty |
| 4 | 79 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1075 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3WFI · The crystal structure of D-mandelate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E3USM3
- Elsewhere: RCSB PDB 3WFI · PDBe 3WFI · UniProt E3USM3
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